added in 11
added in 11
added in 11
x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()])
penicillins()[!penicillins() %in% betalactams_with_inhibitor()]
See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
MRSA isolates are in this file safely denoted as FOX resistant
penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())]
penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())]
penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())]
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV"))
x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV"))
from flowchart: when OXA < 20 or PEN > 0.06
from flowchart: when OXA < 20 or PEN > 0.06
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2023 & mo_genus(clinical_breakpoints$mo) == Prevotella)]), AMP, SAM, AMX, AMC, PIP, ETP, IPM); sort(x[x %in% betalactams()])
x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2023 & clinical_breakpoints$mo == as.mo(Fusobacterium necrophorum))]), AMP, SAM, AMX, AMC, PIP, ETP, IPM); sort(x[x %in% betalactams()])
x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2023 & clinical_breakpoints$mo == as.mo(Fusobacterium necrophorum))]), AMP, SAM, AMX, AMC, PIP, ETP, IPM); sort(x[x %in% betalactams()])
x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2023 & clinical_breakpoints$mo == as.mo(Cutibacterium acnes))]), AMP, SAM, AMX, AMC, PIP, ETP, IPM, TZP, CTX, CRO); sort(x[x %in% betalactams()])
x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2022 & clinical_breakpoints$mo == as.mo(H. influenzae))]), IMR, MEV); sort(x[x %in% betalactams()])
penicillins()[!penicillins() %in% betalactams_with_inhibitor()]
See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
MRSA isolates are in this file safely denoted as FOX resistant
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2022 & clinical_breakpoints$mo == as.mo(S. pneumoniae) & clinical_breakpoints$ab != as.ab(cefaclor))]); sort(c(x[x %in% betalactams()], SAM, PIP, TZP, PHN, IMR, MEV))
x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2022 & clinical_breakpoints$mo == as.mo(S. pneumoniae) & clinical_breakpoints$ab != as.ab(cefaclor))]); sort(c(x[x %in% betalactams()], SAM, PIP, TZP, PHN, IMR, MEV))
from flowchart: when OXA < 20 or PEN > 0.06
from flowchart: when OXA < 20 or PEN > 0.06
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
will be expanded in eucast_rules()
will be expanded in eucast_rules()
will be expanded in eucast_rules()
will be expanded in eucast_rules()
will be expanded in eucast_rules()
x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2024 & mo_genus(clinical_breakpoints$mo) == Prevotella)]), AMP, SAM, AMX, AMC, PIP, ETP, IPM); sort(x[x %in% betalactams()])
x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2024 & clinical_breakpoints$mo == as.mo(Fusobacterium necrophorum))]), AMP, SAM, AMX, AMC, PIP, ETP, IPM); sort(x[x %in% betalactams()])
x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2024 & clinical_breakpoints$mo == as.mo(Fusobacterium necrophorum))]), AMP, SAM, AMX, AMC, PIP, ETP, IPM); sort(x[x %in% betalactams()])
x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2024 & clinical_breakpoints$mo == as.mo(Cutibacterium acnes))]), AMP, SAM, AMX, AMC, PIP, ETP, IPM, TZP, CTX, CRO); sort(x[x %in% betalactams()])
x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2022 & clinical_breakpoints$mo == as.mo(H. influenzae))]), IMR, MEV); sort(x[x %in% betalactams()])
penicillins()[!penicillins() %in% betalactams_with_inhibitor()]
See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
MRSA isolates are in this file safely denoted as FOX resistant
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2022 & clinical_breakpoints$mo == as.mo(S. pneumoniae) & clinical_breakpoints$ab != as.ab(cefaclor))]); sort(c(x[x %in% betalactams()], SAM, PIP, TZP, PHN, IMR, MEV))
x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2022 & clinical_breakpoints$mo == as.mo(S. pneumoniae) & clinical_breakpoints$ab != as.ab(cefaclor))]); sort(c(x[x %in% betalactams()], SAM, PIP, TZP, PHN, IMR, MEV))
from flowchart: when OXA < 20 or PEN > 0.06
from flowchart: when OXA < 20 or PEN > 0.06
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
will be expanded in eucast_rules()
will be expanded in eucast_rules()
will be expanded in eucast_rules()
will be expanded in eucast_rules()
will be expanded in eucast_rules()
x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2024 & mo_genus(clinical_breakpoints$mo) == Prevotella)]), AMP, SAM, AMX, AMC, PIP, ETP, IPM); sort(x[x %in% betalactams()])
x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2024 & clinical_breakpoints$mo == as.mo(Fusobacterium necrophorum))]), AMP, SAM, AMX, AMC, PIP, ETP, IPM); sort(x[x %in% betalactams()])
x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2024 & clinical_breakpoints$mo == as.mo(Fusobacterium necrophorum))]), AMP, SAM, AMX, AMC, PIP, ETP, IPM); sort(x[x %in% betalactams()])
x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2024 & clinical_breakpoints$mo == as.mo(Cutibacterium acnes))]), AMP, SAM, AMX, AMC, PIP, ETP, IPM, TZP, CTX, CRO); sort(x[x %in% betalactams()])
x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2022 & clinical_breakpoints$mo == as.mo(H. influenzae))]), IMR, MEV); sort(x[x %in% betalactams()])
penicillins()[!penicillins() %in% betalactams_with_inhibitor()]
See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2022 & clinical_breakpoints$mo == as.mo(S. pneumoniae) & clinical_breakpoints$ab != as.ab(cefaclor))]); sort(c(x[x %in% betalactams()], SAM, PIP, TZP, PHN, IMR, MEV))
x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2022 & clinical_breakpoints$mo == as.mo(S. pneumoniae) & clinical_breakpoints$ab != as.ab(cefaclor))]); sort(c(x[x %in% betalactams()], SAM, PIP, TZP, PHN, IMR, MEV))
from flowchart: when OXA < 20 or PEN > 0.06
from flowchart: when OXA < 20 or PEN > 0.06
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
MO group name will be expanded in eucast_rules()
MO group name will be expanded in eucast_rules()
MO group name will be expanded in eucast_rules()
MO group name will be expanded in eucast_rules()
MO group name will be expanded in eucast_rules()
x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & mo_genus(clinical_breakpoints$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Cutibacterium acnes"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM", "TZP", "CTX", "CRO"); sort(x[x %in% betalactams()])
originally Enterobacter aerogenes, but was renamed to Klebsiella aerogenes
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
These last ones are all true sulfonamides
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
These last ones are all true sulfonamides
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
These last ones are all true sulfonamides
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
This is Enterobacterales except Salmonella spp.
This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
all penicillins without beta-lactamse inhibitor
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
These last ones are all true sulfonamides
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
These last ones are all true sulfonamides
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
These last ones are all true sulfonamides
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
This is Enterobacterales except Salmonella spp.
This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
all penicillins without beta-lactamse inhibitor